An Analysis of Gene Regulatory Network Topology Using Results of DNA Microchip Experiments

Abstract

In this paper, we have presented the research results concerning analysis of gene regulatory network structure based on Cytoscape software tools using graph theory. The gene regulatory network reconstructed using gene expression profiles of patients which were investigated on Alzheimer disease was used as an experimental one during the simulation process. The analysis process was performed by calculation of both the simple and distributed topological parameters which determine the network structure and the character of the appropriate simple parameters dependence between each other respectively. The objective of the research is development of the technique of gene regulatory network topology optimization based on complex use of the network topological parameters. The methods based on graph theory and multicriterial optimization technique were used for data processing during the simulation process. The charts of both the simple and distributed topological parameters were created as the result of the simulation. The final decision concerning choice of the optimal network topology was done based on complex topological index which was calculated using Harrington desirability function. The simulation results analysis has allowed determining the optimal strategy of gene regulatory networks reconstruction based on gene expression profiles with following development of effective technique of reconstructed networks validation based on analysis of appropriate networks topological parameters.KeywordsMulticriterial optimizationDecision makingGraph theoryTopological parametersGene regulatory network topologyDNA microchips